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<FONT color="green">001</FONT>    /*<a name="line.1"></a>
<FONT color="green">002</FONT>     * Licensed to the Apache Software Foundation (ASF) under one or more<a name="line.2"></a>
<FONT color="green">003</FONT>     * contributor license agreements.  See the NOTICE file distributed with<a name="line.3"></a>
<FONT color="green">004</FONT>     * this work for additional information regarding copyright ownership.<a name="line.4"></a>
<FONT color="green">005</FONT>     * The ASF licenses this file to You under the Apache License, Version 2.0<a name="line.5"></a>
<FONT color="green">006</FONT>     * (the "License"); you may not use this file except in compliance with<a name="line.6"></a>
<FONT color="green">007</FONT>     * the License.  You may obtain a copy of the License at<a name="line.7"></a>
<FONT color="green">008</FONT>     *<a name="line.8"></a>
<FONT color="green">009</FONT>     *      http://www.apache.org/licenses/LICENSE-2.0<a name="line.9"></a>
<FONT color="green">010</FONT>     *<a name="line.10"></a>
<FONT color="green">011</FONT>     * Unless required by applicable law or agreed to in writing, software<a name="line.11"></a>
<FONT color="green">012</FONT>     * distributed under the License is distributed on an "AS IS" BASIS,<a name="line.12"></a>
<FONT color="green">013</FONT>     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.<a name="line.13"></a>
<FONT color="green">014</FONT>     * See the License for the specific language governing permissions and<a name="line.14"></a>
<FONT color="green">015</FONT>     * limitations under the License.<a name="line.15"></a>
<FONT color="green">016</FONT>     */<a name="line.16"></a>
<FONT color="green">017</FONT>    <a name="line.17"></a>
<FONT color="green">018</FONT>    package org.apache.commons.math.stat.ranking;<a name="line.18"></a>
<FONT color="green">019</FONT>    <a name="line.19"></a>
<FONT color="green">020</FONT>    import java.util.ArrayList;<a name="line.20"></a>
<FONT color="green">021</FONT>    import java.util.Arrays;<a name="line.21"></a>
<FONT color="green">022</FONT>    import java.util.Iterator;<a name="line.22"></a>
<FONT color="green">023</FONT>    import java.util.List;<a name="line.23"></a>
<FONT color="green">024</FONT>    <a name="line.24"></a>
<FONT color="green">025</FONT>    import org.apache.commons.math.exception.MathInternalError;<a name="line.25"></a>
<FONT color="green">026</FONT>    import org.apache.commons.math.random.RandomData;<a name="line.26"></a>
<FONT color="green">027</FONT>    import org.apache.commons.math.random.RandomDataImpl;<a name="line.27"></a>
<FONT color="green">028</FONT>    import org.apache.commons.math.random.RandomGenerator;<a name="line.28"></a>
<FONT color="green">029</FONT>    import org.apache.commons.math.util.FastMath;<a name="line.29"></a>
<FONT color="green">030</FONT>    <a name="line.30"></a>
<FONT color="green">031</FONT>    <a name="line.31"></a>
<FONT color="green">032</FONT>    /**<a name="line.32"></a>
<FONT color="green">033</FONT>     * &lt;p&gt; Ranking based on the natural ordering on doubles.&lt;/p&gt;<a name="line.33"></a>
<FONT color="green">034</FONT>     * &lt;p&gt;NaNs are treated according to the configured {@link NaNStrategy} and ties<a name="line.34"></a>
<FONT color="green">035</FONT>     * are handled using the selected {@link TiesStrategy}.<a name="line.35"></a>
<FONT color="green">036</FONT>     * Configuration settings are supplied in optional constructor arguments.<a name="line.36"></a>
<FONT color="green">037</FONT>     * Defaults are {@link NaNStrategy#MAXIMAL} and {@link TiesStrategy#AVERAGE},<a name="line.37"></a>
<FONT color="green">038</FONT>     * respectively. When using {@link TiesStrategy#RANDOM}, a<a name="line.38"></a>
<FONT color="green">039</FONT>     * {@link RandomGenerator} may be supplied as a constructor argument.&lt;/p&gt;<a name="line.39"></a>
<FONT color="green">040</FONT>     * &lt;p&gt;Examples:<a name="line.40"></a>
<FONT color="green">041</FONT>     * &lt;table border="1" cellpadding="3"&gt;<a name="line.41"></a>
<FONT color="green">042</FONT>     * &lt;tr&gt;&lt;th colspan="3"&gt;<a name="line.42"></a>
<FONT color="green">043</FONT>     * Input data: (20, 17, 30, 42.3, 17, 50, Double.NaN, Double.NEGATIVE_INFINITY, 17)<a name="line.43"></a>
<FONT color="green">044</FONT>     * &lt;/th&gt;&lt;/tr&gt;<a name="line.44"></a>
<FONT color="green">045</FONT>     * &lt;tr&gt;&lt;th&gt;NaNStrategy&lt;/th&gt;&lt;th&gt;TiesStrategy&lt;/th&gt;<a name="line.45"></a>
<FONT color="green">046</FONT>     * &lt;th&gt;&lt;code&gt;rank(data)&lt;/code&gt;&lt;/th&gt;<a name="line.46"></a>
<FONT color="green">047</FONT>     * &lt;tr&gt;<a name="line.47"></a>
<FONT color="green">048</FONT>     * &lt;td&gt;default (NaNs maximal)&lt;/td&gt;<a name="line.48"></a>
<FONT color="green">049</FONT>     * &lt;td&gt;default (ties averaged)&lt;/td&gt;<a name="line.49"></a>
<FONT color="green">050</FONT>     * &lt;td&gt;(5, 3, 6, 7, 3, 8, 9, 1, 3)&lt;/td&gt;&lt;/tr&gt;<a name="line.50"></a>
<FONT color="green">051</FONT>     * &lt;tr&gt;<a name="line.51"></a>
<FONT color="green">052</FONT>     * &lt;td&gt;default (NaNs maximal)&lt;/td&gt;<a name="line.52"></a>
<FONT color="green">053</FONT>     * &lt;td&gt;MINIMUM&lt;/td&gt;<a name="line.53"></a>
<FONT color="green">054</FONT>     * &lt;td&gt;(5, 2, 6, 7, 2, 8, 9, 1, 2)&lt;/td&gt;&lt;/tr&gt;<a name="line.54"></a>
<FONT color="green">055</FONT>     * &lt;tr&gt;<a name="line.55"></a>
<FONT color="green">056</FONT>     * &lt;td&gt;MINIMAL&lt;/td&gt;<a name="line.56"></a>
<FONT color="green">057</FONT>     * &lt;td&gt;default (ties averaged)&lt;/td&gt;<a name="line.57"></a>
<FONT color="green">058</FONT>     * &lt;td&gt;(6, 4, 7, 8, 4, 9, 1.5, 1.5, 4)&lt;/td&gt;&lt;/tr&gt;<a name="line.58"></a>
<FONT color="green">059</FONT>     * &lt;tr&gt;<a name="line.59"></a>
<FONT color="green">060</FONT>     * &lt;td&gt;REMOVED&lt;/td&gt;<a name="line.60"></a>
<FONT color="green">061</FONT>     * &lt;td&gt;SEQUENTIAL&lt;/td&gt;<a name="line.61"></a>
<FONT color="green">062</FONT>     * &lt;td&gt;(5, 2, 6, 7, 3, 8, 1, 4)&lt;/td&gt;&lt;/tr&gt;<a name="line.62"></a>
<FONT color="green">063</FONT>     * &lt;tr&gt;<a name="line.63"></a>
<FONT color="green">064</FONT>     * &lt;td&gt;MINIMAL&lt;/td&gt;<a name="line.64"></a>
<FONT color="green">065</FONT>     * &lt;td&gt;MAXIMUM&lt;/td&gt;<a name="line.65"></a>
<FONT color="green">066</FONT>     * &lt;td&gt;(6, 5, 7, 8, 5, 9, 2, 2, 5)&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;&lt;/p&gt;<a name="line.66"></a>
<FONT color="green">067</FONT>     *<a name="line.67"></a>
<FONT color="green">068</FONT>     * @since 2.0<a name="line.68"></a>
<FONT color="green">069</FONT>     * @version $Revision: 1061496 $ $Date: 2011-01-20 21:32:16 +0100 (jeu. 20 janv. 2011) $<a name="line.69"></a>
<FONT color="green">070</FONT>     */<a name="line.70"></a>
<FONT color="green">071</FONT>    public class NaturalRanking implements RankingAlgorithm {<a name="line.71"></a>
<FONT color="green">072</FONT>    <a name="line.72"></a>
<FONT color="green">073</FONT>        /** default NaN strategy */<a name="line.73"></a>
<FONT color="green">074</FONT>        public static final NaNStrategy DEFAULT_NAN_STRATEGY = NaNStrategy.MAXIMAL;<a name="line.74"></a>
<FONT color="green">075</FONT>    <a name="line.75"></a>
<FONT color="green">076</FONT>        /** default ties strategy */<a name="line.76"></a>
<FONT color="green">077</FONT>        public static final TiesStrategy DEFAULT_TIES_STRATEGY = TiesStrategy.AVERAGE;<a name="line.77"></a>
<FONT color="green">078</FONT>    <a name="line.78"></a>
<FONT color="green">079</FONT>        /** NaN strategy - defaults to NaNs maximal */<a name="line.79"></a>
<FONT color="green">080</FONT>        private final NaNStrategy nanStrategy;<a name="line.80"></a>
<FONT color="green">081</FONT>    <a name="line.81"></a>
<FONT color="green">082</FONT>        /** Ties strategy - defaults to ties averaged */<a name="line.82"></a>
<FONT color="green">083</FONT>        private final TiesStrategy tiesStrategy;<a name="line.83"></a>
<FONT color="green">084</FONT>    <a name="line.84"></a>
<FONT color="green">085</FONT>        /** Source of random data - used only when ties strategy is RANDOM */<a name="line.85"></a>
<FONT color="green">086</FONT>        private final RandomData randomData;<a name="line.86"></a>
<FONT color="green">087</FONT>    <a name="line.87"></a>
<FONT color="green">088</FONT>        /**<a name="line.88"></a>
<FONT color="green">089</FONT>         * Create a NaturalRanking with default strategies for handling ties and NaNs.<a name="line.89"></a>
<FONT color="green">090</FONT>         */<a name="line.90"></a>
<FONT color="green">091</FONT>        public NaturalRanking() {<a name="line.91"></a>
<FONT color="green">092</FONT>            super();<a name="line.92"></a>
<FONT color="green">093</FONT>            tiesStrategy = DEFAULT_TIES_STRATEGY;<a name="line.93"></a>
<FONT color="green">094</FONT>            nanStrategy = DEFAULT_NAN_STRATEGY;<a name="line.94"></a>
<FONT color="green">095</FONT>            randomData = null;<a name="line.95"></a>
<FONT color="green">096</FONT>        }<a name="line.96"></a>
<FONT color="green">097</FONT>    <a name="line.97"></a>
<FONT color="green">098</FONT>        /**<a name="line.98"></a>
<FONT color="green">099</FONT>         * Create a NaturalRanking with the given TiesStrategy.<a name="line.99"></a>
<FONT color="green">100</FONT>         *<a name="line.100"></a>
<FONT color="green">101</FONT>         * @param tiesStrategy the TiesStrategy to use<a name="line.101"></a>
<FONT color="green">102</FONT>         */<a name="line.102"></a>
<FONT color="green">103</FONT>        public NaturalRanking(TiesStrategy tiesStrategy) {<a name="line.103"></a>
<FONT color="green">104</FONT>            super();<a name="line.104"></a>
<FONT color="green">105</FONT>            this.tiesStrategy = tiesStrategy;<a name="line.105"></a>
<FONT color="green">106</FONT>            nanStrategy = DEFAULT_NAN_STRATEGY;<a name="line.106"></a>
<FONT color="green">107</FONT>            randomData = new RandomDataImpl();<a name="line.107"></a>
<FONT color="green">108</FONT>        }<a name="line.108"></a>
<FONT color="green">109</FONT>    <a name="line.109"></a>
<FONT color="green">110</FONT>        /**<a name="line.110"></a>
<FONT color="green">111</FONT>         * Create a NaturalRanking with the given NaNStrategy.<a name="line.111"></a>
<FONT color="green">112</FONT>         *<a name="line.112"></a>
<FONT color="green">113</FONT>         * @param nanStrategy the NaNStrategy to use<a name="line.113"></a>
<FONT color="green">114</FONT>         */<a name="line.114"></a>
<FONT color="green">115</FONT>        public NaturalRanking(NaNStrategy nanStrategy) {<a name="line.115"></a>
<FONT color="green">116</FONT>            super();<a name="line.116"></a>
<FONT color="green">117</FONT>            this.nanStrategy = nanStrategy;<a name="line.117"></a>
<FONT color="green">118</FONT>            tiesStrategy = DEFAULT_TIES_STRATEGY;<a name="line.118"></a>
<FONT color="green">119</FONT>            randomData = null;<a name="line.119"></a>
<FONT color="green">120</FONT>        }<a name="line.120"></a>
<FONT color="green">121</FONT>    <a name="line.121"></a>
<FONT color="green">122</FONT>        /**<a name="line.122"></a>
<FONT color="green">123</FONT>         * Create a NaturalRanking with the given NaNStrategy and TiesStrategy.<a name="line.123"></a>
<FONT color="green">124</FONT>         *<a name="line.124"></a>
<FONT color="green">125</FONT>         * @param nanStrategy NaNStrategy to use<a name="line.125"></a>
<FONT color="green">126</FONT>         * @param tiesStrategy TiesStrategy to use<a name="line.126"></a>
<FONT color="green">127</FONT>         */<a name="line.127"></a>
<FONT color="green">128</FONT>        public NaturalRanking(NaNStrategy nanStrategy, TiesStrategy tiesStrategy) {<a name="line.128"></a>
<FONT color="green">129</FONT>            super();<a name="line.129"></a>
<FONT color="green">130</FONT>            this.nanStrategy = nanStrategy;<a name="line.130"></a>
<FONT color="green">131</FONT>            this.tiesStrategy = tiesStrategy;<a name="line.131"></a>
<FONT color="green">132</FONT>            randomData = new RandomDataImpl();<a name="line.132"></a>
<FONT color="green">133</FONT>        }<a name="line.133"></a>
<FONT color="green">134</FONT>    <a name="line.134"></a>
<FONT color="green">135</FONT>        /**<a name="line.135"></a>
<FONT color="green">136</FONT>         * Create a NaturalRanking with TiesStrategy.RANDOM and the given<a name="line.136"></a>
<FONT color="green">137</FONT>         * RandomGenerator as the source of random data.<a name="line.137"></a>
<FONT color="green">138</FONT>         *<a name="line.138"></a>
<FONT color="green">139</FONT>         * @param randomGenerator source of random data<a name="line.139"></a>
<FONT color="green">140</FONT>         */<a name="line.140"></a>
<FONT color="green">141</FONT>        public NaturalRanking(RandomGenerator randomGenerator) {<a name="line.141"></a>
<FONT color="green">142</FONT>            super();<a name="line.142"></a>
<FONT color="green">143</FONT>            this.tiesStrategy = TiesStrategy.RANDOM;<a name="line.143"></a>
<FONT color="green">144</FONT>            nanStrategy = DEFAULT_NAN_STRATEGY;<a name="line.144"></a>
<FONT color="green">145</FONT>            randomData = new RandomDataImpl(randomGenerator);<a name="line.145"></a>
<FONT color="green">146</FONT>        }<a name="line.146"></a>
<FONT color="green">147</FONT>    <a name="line.147"></a>
<FONT color="green">148</FONT>    <a name="line.148"></a>
<FONT color="green">149</FONT>        /**<a name="line.149"></a>
<FONT color="green">150</FONT>         * Create a NaturalRanking with the given NaNStrategy, TiesStrategy.RANDOM<a name="line.150"></a>
<FONT color="green">151</FONT>         * and the given source of random data.<a name="line.151"></a>
<FONT color="green">152</FONT>         *<a name="line.152"></a>
<FONT color="green">153</FONT>         * @param nanStrategy NaNStrategy to use<a name="line.153"></a>
<FONT color="green">154</FONT>         * @param randomGenerator source of random data<a name="line.154"></a>
<FONT color="green">155</FONT>         */<a name="line.155"></a>
<FONT color="green">156</FONT>        public NaturalRanking(NaNStrategy nanStrategy,<a name="line.156"></a>
<FONT color="green">157</FONT>                RandomGenerator randomGenerator) {<a name="line.157"></a>
<FONT color="green">158</FONT>            super();<a name="line.158"></a>
<FONT color="green">159</FONT>            this.nanStrategy = nanStrategy;<a name="line.159"></a>
<FONT color="green">160</FONT>            this.tiesStrategy = TiesStrategy.RANDOM;<a name="line.160"></a>
<FONT color="green">161</FONT>            randomData = new RandomDataImpl(randomGenerator);<a name="line.161"></a>
<FONT color="green">162</FONT>        }<a name="line.162"></a>
<FONT color="green">163</FONT>    <a name="line.163"></a>
<FONT color="green">164</FONT>        /**<a name="line.164"></a>
<FONT color="green">165</FONT>         * Return the NaNStrategy<a name="line.165"></a>
<FONT color="green">166</FONT>         *<a name="line.166"></a>
<FONT color="green">167</FONT>         * @return returns the NaNStrategy<a name="line.167"></a>
<FONT color="green">168</FONT>         */<a name="line.168"></a>
<FONT color="green">169</FONT>        public NaNStrategy getNanStrategy() {<a name="line.169"></a>
<FONT color="green">170</FONT>            return nanStrategy;<a name="line.170"></a>
<FONT color="green">171</FONT>        }<a name="line.171"></a>
<FONT color="green">172</FONT>    <a name="line.172"></a>
<FONT color="green">173</FONT>        /**<a name="line.173"></a>
<FONT color="green">174</FONT>         * Return the TiesStrategy<a name="line.174"></a>
<FONT color="green">175</FONT>         *<a name="line.175"></a>
<FONT color="green">176</FONT>         * @return the TiesStrategy<a name="line.176"></a>
<FONT color="green">177</FONT>         */<a name="line.177"></a>
<FONT color="green">178</FONT>        public TiesStrategy getTiesStrategy() {<a name="line.178"></a>
<FONT color="green">179</FONT>            return tiesStrategy;<a name="line.179"></a>
<FONT color="green">180</FONT>        }<a name="line.180"></a>
<FONT color="green">181</FONT>    <a name="line.181"></a>
<FONT color="green">182</FONT>        /**<a name="line.182"></a>
<FONT color="green">183</FONT>         * Rank &lt;code&gt;data&lt;/code&gt; using the natural ordering on Doubles, with<a name="line.183"></a>
<FONT color="green">184</FONT>         * NaN values handled according to &lt;code&gt;nanStrategy&lt;/code&gt; and ties<a name="line.184"></a>
<FONT color="green">185</FONT>         * resolved using &lt;code&gt;tiesStrategy.&lt;/code&gt;<a name="line.185"></a>
<FONT color="green">186</FONT>         *<a name="line.186"></a>
<FONT color="green">187</FONT>         * @param data array to be ranked<a name="line.187"></a>
<FONT color="green">188</FONT>         * @return array of ranks<a name="line.188"></a>
<FONT color="green">189</FONT>         */<a name="line.189"></a>
<FONT color="green">190</FONT>        public double[] rank(double[] data) {<a name="line.190"></a>
<FONT color="green">191</FONT>    <a name="line.191"></a>
<FONT color="green">192</FONT>            // Array recording initial positions of data to be ranked<a name="line.192"></a>
<FONT color="green">193</FONT>            IntDoublePair[] ranks = new IntDoublePair[data.length];<a name="line.193"></a>
<FONT color="green">194</FONT>            for (int i = 0; i &lt; data.length; i++) {<a name="line.194"></a>
<FONT color="green">195</FONT>                ranks[i] = new IntDoublePair(data[i], i);<a name="line.195"></a>
<FONT color="green">196</FONT>            }<a name="line.196"></a>
<FONT color="green">197</FONT>    <a name="line.197"></a>
<FONT color="green">198</FONT>            // Recode, remove or record positions of NaNs<a name="line.198"></a>
<FONT color="green">199</FONT>            List&lt;Integer&gt; nanPositions = null;<a name="line.199"></a>
<FONT color="green">200</FONT>            switch (nanStrategy) {<a name="line.200"></a>
<FONT color="green">201</FONT>                case MAXIMAL: // Replace NaNs with +INFs<a name="line.201"></a>
<FONT color="green">202</FONT>                    recodeNaNs(ranks, Double.POSITIVE_INFINITY);<a name="line.202"></a>
<FONT color="green">203</FONT>                    break;<a name="line.203"></a>
<FONT color="green">204</FONT>                case MINIMAL: // Replace NaNs with -INFs<a name="line.204"></a>
<FONT color="green">205</FONT>                    recodeNaNs(ranks, Double.NEGATIVE_INFINITY);<a name="line.205"></a>
<FONT color="green">206</FONT>                    break;<a name="line.206"></a>
<FONT color="green">207</FONT>                case REMOVED: // Drop NaNs from data<a name="line.207"></a>
<FONT color="green">208</FONT>                    ranks = removeNaNs(ranks);<a name="line.208"></a>
<FONT color="green">209</FONT>                    break;<a name="line.209"></a>
<FONT color="green">210</FONT>                case FIXED:   // Record positions of NaNs<a name="line.210"></a>
<FONT color="green">211</FONT>                    nanPositions = getNanPositions(ranks);<a name="line.211"></a>
<FONT color="green">212</FONT>                    break;<a name="line.212"></a>
<FONT color="green">213</FONT>                default: // this should not happen unless NaNStrategy enum is changed<a name="line.213"></a>
<FONT color="green">214</FONT>                    throw new MathInternalError();<a name="line.214"></a>
<FONT color="green">215</FONT>            }<a name="line.215"></a>
<FONT color="green">216</FONT>    <a name="line.216"></a>
<FONT color="green">217</FONT>            // Sort the IntDoublePairs<a name="line.217"></a>
<FONT color="green">218</FONT>            Arrays.sort(ranks);<a name="line.218"></a>
<FONT color="green">219</FONT>    <a name="line.219"></a>
<FONT color="green">220</FONT>            // Walk the sorted array, filling output array using sorted positions,<a name="line.220"></a>
<FONT color="green">221</FONT>            // resolving ties as we go<a name="line.221"></a>
<FONT color="green">222</FONT>            double[] out = new double[ranks.length];<a name="line.222"></a>
<FONT color="green">223</FONT>            int pos = 1;  // position in sorted array<a name="line.223"></a>
<FONT color="green">224</FONT>            out[ranks[0].getPosition()] = pos;<a name="line.224"></a>
<FONT color="green">225</FONT>            List&lt;Integer&gt; tiesTrace = new ArrayList&lt;Integer&gt;();<a name="line.225"></a>
<FONT color="green">226</FONT>            tiesTrace.add(ranks[0].getPosition());<a name="line.226"></a>
<FONT color="green">227</FONT>            for (int i = 1; i &lt; ranks.length; i++) {<a name="line.227"></a>
<FONT color="green">228</FONT>                if (Double.compare(ranks[i].getValue(), ranks[i - 1].getValue()) &gt; 0) {<a name="line.228"></a>
<FONT color="green">229</FONT>                    // tie sequence has ended (or had length 1)<a name="line.229"></a>
<FONT color="green">230</FONT>                    pos = i + 1;<a name="line.230"></a>
<FONT color="green">231</FONT>                    if (tiesTrace.size() &gt; 1) {  // if seq is nontrivial, resolve<a name="line.231"></a>
<FONT color="green">232</FONT>                        resolveTie(out, tiesTrace);<a name="line.232"></a>
<FONT color="green">233</FONT>                    }<a name="line.233"></a>
<FONT color="green">234</FONT>                    tiesTrace = new ArrayList&lt;Integer&gt;();<a name="line.234"></a>
<FONT color="green">235</FONT>                    tiesTrace.add(ranks[i].getPosition());<a name="line.235"></a>
<FONT color="green">236</FONT>                } else {<a name="line.236"></a>
<FONT color="green">237</FONT>                    // tie sequence continues<a name="line.237"></a>
<FONT color="green">238</FONT>                    tiesTrace.add(ranks[i].getPosition());<a name="line.238"></a>
<FONT color="green">239</FONT>                }<a name="line.239"></a>
<FONT color="green">240</FONT>                out[ranks[i].getPosition()] = pos;<a name="line.240"></a>
<FONT color="green">241</FONT>            }<a name="line.241"></a>
<FONT color="green">242</FONT>            if (tiesTrace.size() &gt; 1) {  // handle tie sequence at end<a name="line.242"></a>
<FONT color="green">243</FONT>                resolveTie(out, tiesTrace);<a name="line.243"></a>
<FONT color="green">244</FONT>            }<a name="line.244"></a>
<FONT color="green">245</FONT>            if (nanStrategy == NaNStrategy.FIXED) {<a name="line.245"></a>
<FONT color="green">246</FONT>                restoreNaNs(out, nanPositions);<a name="line.246"></a>
<FONT color="green">247</FONT>            }<a name="line.247"></a>
<FONT color="green">248</FONT>            return out;<a name="line.248"></a>
<FONT color="green">249</FONT>        }<a name="line.249"></a>
<FONT color="green">250</FONT>    <a name="line.250"></a>
<FONT color="green">251</FONT>        /**<a name="line.251"></a>
<FONT color="green">252</FONT>         * Returns an array that is a copy of the input array with IntDoublePairs<a name="line.252"></a>
<FONT color="green">253</FONT>         * having NaN values removed.<a name="line.253"></a>
<FONT color="green">254</FONT>         *<a name="line.254"></a>
<FONT color="green">255</FONT>         * @param ranks input array<a name="line.255"></a>
<FONT color="green">256</FONT>         * @return array with NaN-valued entries removed<a name="line.256"></a>
<FONT color="green">257</FONT>         */<a name="line.257"></a>
<FONT color="green">258</FONT>        private IntDoublePair[] removeNaNs(IntDoublePair[] ranks) {<a name="line.258"></a>
<FONT color="green">259</FONT>            if (!containsNaNs(ranks)) {<a name="line.259"></a>
<FONT color="green">260</FONT>                return ranks;<a name="line.260"></a>
<FONT color="green">261</FONT>            }<a name="line.261"></a>
<FONT color="green">262</FONT>            IntDoublePair[] outRanks = new IntDoublePair[ranks.length];<a name="line.262"></a>
<FONT color="green">263</FONT>            int j = 0;<a name="line.263"></a>
<FONT color="green">264</FONT>            for (int i = 0; i &lt; ranks.length; i++) {<a name="line.264"></a>
<FONT color="green">265</FONT>                if (Double.isNaN(ranks[i].getValue())) {<a name="line.265"></a>
<FONT color="green">266</FONT>                    // drop, but adjust original ranks of later elements<a name="line.266"></a>
<FONT color="green">267</FONT>                    for (int k = i + 1; k &lt; ranks.length; k++) {<a name="line.267"></a>
<FONT color="green">268</FONT>                        ranks[k] = new IntDoublePair(<a name="line.268"></a>
<FONT color="green">269</FONT>                                ranks[k].getValue(), ranks[k].getPosition() - 1);<a name="line.269"></a>
<FONT color="green">270</FONT>                    }<a name="line.270"></a>
<FONT color="green">271</FONT>                } else {<a name="line.271"></a>
<FONT color="green">272</FONT>                    outRanks[j] = new IntDoublePair(<a name="line.272"></a>
<FONT color="green">273</FONT>                            ranks[i].getValue(), ranks[i].getPosition());<a name="line.273"></a>
<FONT color="green">274</FONT>                    j++;<a name="line.274"></a>
<FONT color="green">275</FONT>                }<a name="line.275"></a>
<FONT color="green">276</FONT>            }<a name="line.276"></a>
<FONT color="green">277</FONT>            IntDoublePair[] returnRanks = new IntDoublePair[j];<a name="line.277"></a>
<FONT color="green">278</FONT>            System.arraycopy(outRanks, 0, returnRanks, 0, j);<a name="line.278"></a>
<FONT color="green">279</FONT>            return returnRanks;<a name="line.279"></a>
<FONT color="green">280</FONT>        }<a name="line.280"></a>
<FONT color="green">281</FONT>    <a name="line.281"></a>
<FONT color="green">282</FONT>        /**<a name="line.282"></a>
<FONT color="green">283</FONT>         * Recodes NaN values to the given value.<a name="line.283"></a>
<FONT color="green">284</FONT>         *<a name="line.284"></a>
<FONT color="green">285</FONT>         * @param ranks array to recode<a name="line.285"></a>
<FONT color="green">286</FONT>         * @param value the value to replace NaNs with<a name="line.286"></a>
<FONT color="green">287</FONT>         */<a name="line.287"></a>
<FONT color="green">288</FONT>        private void recodeNaNs(IntDoublePair[] ranks, double value) {<a name="line.288"></a>
<FONT color="green">289</FONT>            for (int i = 0; i &lt; ranks.length; i++) {<a name="line.289"></a>
<FONT color="green">290</FONT>                if (Double.isNaN(ranks[i].getValue())) {<a name="line.290"></a>
<FONT color="green">291</FONT>                    ranks[i] = new IntDoublePair(<a name="line.291"></a>
<FONT color="green">292</FONT>                            value, ranks[i].getPosition());<a name="line.292"></a>
<FONT color="green">293</FONT>                }<a name="line.293"></a>
<FONT color="green">294</FONT>            }<a name="line.294"></a>
<FONT color="green">295</FONT>        }<a name="line.295"></a>
<FONT color="green">296</FONT>    <a name="line.296"></a>
<FONT color="green">297</FONT>        /**<a name="line.297"></a>
<FONT color="green">298</FONT>         * Checks for presence of NaNs in &lt;code&gt;ranks.&lt;/code&gt;<a name="line.298"></a>
<FONT color="green">299</FONT>         *<a name="line.299"></a>
<FONT color="green">300</FONT>         * @param ranks array to be searched for NaNs<a name="line.300"></a>
<FONT color="green">301</FONT>         * @return true iff ranks contains one or more NaNs<a name="line.301"></a>
<FONT color="green">302</FONT>         */<a name="line.302"></a>
<FONT color="green">303</FONT>        private boolean containsNaNs(IntDoublePair[] ranks) {<a name="line.303"></a>
<FONT color="green">304</FONT>            for (int i = 0; i &lt; ranks.length; i++) {<a name="line.304"></a>
<FONT color="green">305</FONT>                if (Double.isNaN(ranks[i].getValue())) {<a name="line.305"></a>
<FONT color="green">306</FONT>                    return true;<a name="line.306"></a>
<FONT color="green">307</FONT>                }<a name="line.307"></a>
<FONT color="green">308</FONT>            }<a name="line.308"></a>
<FONT color="green">309</FONT>            return false;<a name="line.309"></a>
<FONT color="green">310</FONT>        }<a name="line.310"></a>
<FONT color="green">311</FONT>    <a name="line.311"></a>
<FONT color="green">312</FONT>        /**<a name="line.312"></a>
<FONT color="green">313</FONT>         * Resolve a sequence of ties, using the configured {@link TiesStrategy}.<a name="line.313"></a>
<FONT color="green">314</FONT>         * The input &lt;code&gt;ranks&lt;/code&gt; array is expected to take the same value<a name="line.314"></a>
<FONT color="green">315</FONT>         * for all indices in &lt;code&gt;tiesTrace&lt;/code&gt;.  The common value is recoded<a name="line.315"></a>
<FONT color="green">316</FONT>         * according to the tiesStrategy. For example, if ranks = &lt;5,8,2,6,2,7,1,2&gt;,<a name="line.316"></a>
<FONT color="green">317</FONT>         * tiesTrace = &lt;2,4,7&gt; and tiesStrategy is MINIMUM, ranks will be unchanged.<a name="line.317"></a>
<FONT color="green">318</FONT>         * The same array and trace with tiesStrategy AVERAGE will come out<a name="line.318"></a>
<FONT color="green">319</FONT>         * &lt;5,8,3,6,3,7,1,3&gt;.<a name="line.319"></a>
<FONT color="green">320</FONT>         *<a name="line.320"></a>
<FONT color="green">321</FONT>         * @param ranks array of ranks<a name="line.321"></a>
<FONT color="green">322</FONT>         * @param tiesTrace list of indices where &lt;code&gt;ranks&lt;/code&gt; is constant<a name="line.322"></a>
<FONT color="green">323</FONT>         * -- that is, for any i and j in TiesTrace, &lt;code&gt; ranks[i] == ranks[j]<a name="line.323"></a>
<FONT color="green">324</FONT>         * &lt;/code&gt;<a name="line.324"></a>
<FONT color="green">325</FONT>         */<a name="line.325"></a>
<FONT color="green">326</FONT>        private void resolveTie(double[] ranks, List&lt;Integer&gt; tiesTrace) {<a name="line.326"></a>
<FONT color="green">327</FONT>    <a name="line.327"></a>
<FONT color="green">328</FONT>            // constant value of ranks over tiesTrace<a name="line.328"></a>
<FONT color="green">329</FONT>            final double c = ranks[tiesTrace.get(0)];<a name="line.329"></a>
<FONT color="green">330</FONT>    <a name="line.330"></a>
<FONT color="green">331</FONT>            // length of sequence of tied ranks<a name="line.331"></a>
<FONT color="green">332</FONT>            final int length = tiesTrace.size();<a name="line.332"></a>
<FONT color="green">333</FONT>    <a name="line.333"></a>
<FONT color="green">334</FONT>            switch (tiesStrategy) {<a name="line.334"></a>
<FONT color="green">335</FONT>                case  AVERAGE:  // Replace ranks with average<a name="line.335"></a>
<FONT color="green">336</FONT>                    fill(ranks, tiesTrace, (2 * c + length - 1) / 2d);<a name="line.336"></a>
<FONT color="green">337</FONT>                    break;<a name="line.337"></a>
<FONT color="green">338</FONT>                case MAXIMUM:   // Replace ranks with maximum values<a name="line.338"></a>
<FONT color="green">339</FONT>                    fill(ranks, tiesTrace, c + length - 1);<a name="line.339"></a>
<FONT color="green">340</FONT>                    break;<a name="line.340"></a>
<FONT color="green">341</FONT>                case MINIMUM:   // Replace ties with minimum<a name="line.341"></a>
<FONT color="green">342</FONT>                    fill(ranks, tiesTrace, c);<a name="line.342"></a>
<FONT color="green">343</FONT>                    break;<a name="line.343"></a>
<FONT color="green">344</FONT>                case RANDOM:    // Fill with random integral values in [c, c + length - 1]<a name="line.344"></a>
<FONT color="green">345</FONT>                    Iterator&lt;Integer&gt; iterator = tiesTrace.iterator();<a name="line.345"></a>
<FONT color="green">346</FONT>                    long f = FastMath.round(c);<a name="line.346"></a>
<FONT color="green">347</FONT>                    while (iterator.hasNext()) {<a name="line.347"></a>
<FONT color="green">348</FONT>                        ranks[iterator.next()] =<a name="line.348"></a>
<FONT color="green">349</FONT>                            randomData.nextLong(f, f + length - 1);<a name="line.349"></a>
<FONT color="green">350</FONT>                    }<a name="line.350"></a>
<FONT color="green">351</FONT>                    break;<a name="line.351"></a>
<FONT color="green">352</FONT>                case SEQUENTIAL:  // Fill sequentially from c to c + length - 1<a name="line.352"></a>
<FONT color="green">353</FONT>                    // walk and fill<a name="line.353"></a>
<FONT color="green">354</FONT>                    iterator = tiesTrace.iterator();<a name="line.354"></a>
<FONT color="green">355</FONT>                    f = FastMath.round(c);<a name="line.355"></a>
<FONT color="green">356</FONT>                    int i = 0;<a name="line.356"></a>
<FONT color="green">357</FONT>                    while (iterator.hasNext()) {<a name="line.357"></a>
<FONT color="green">358</FONT>                        ranks[iterator.next()] = f + i++;<a name="line.358"></a>
<FONT color="green">359</FONT>                    }<a name="line.359"></a>
<FONT color="green">360</FONT>                    break;<a name="line.360"></a>
<FONT color="green">361</FONT>                default: // this should not happen unless TiesStrategy enum is changed<a name="line.361"></a>
<FONT color="green">362</FONT>                    throw new MathInternalError();<a name="line.362"></a>
<FONT color="green">363</FONT>            }<a name="line.363"></a>
<FONT color="green">364</FONT>        }<a name="line.364"></a>
<FONT color="green">365</FONT>    <a name="line.365"></a>
<FONT color="green">366</FONT>        /**<a name="line.366"></a>
<FONT color="green">367</FONT>         * Sets&lt;code&gt;data[i] = value&lt;/code&gt; for each i in &lt;code&gt;tiesTrace.&lt;/code&gt;<a name="line.367"></a>
<FONT color="green">368</FONT>         *<a name="line.368"></a>
<FONT color="green">369</FONT>         * @param data array to modify<a name="line.369"></a>
<FONT color="green">370</FONT>         * @param tiesTrace list of index values to set<a name="line.370"></a>
<FONT color="green">371</FONT>         * @param value value to set<a name="line.371"></a>
<FONT color="green">372</FONT>         */<a name="line.372"></a>
<FONT color="green">373</FONT>        private void fill(double[] data, List&lt;Integer&gt; tiesTrace, double value) {<a name="line.373"></a>
<FONT color="green">374</FONT>            Iterator&lt;Integer&gt; iterator = tiesTrace.iterator();<a name="line.374"></a>
<FONT color="green">375</FONT>            while (iterator.hasNext()) {<a name="line.375"></a>
<FONT color="green">376</FONT>                data[iterator.next()] = value;<a name="line.376"></a>
<FONT color="green">377</FONT>            }<a name="line.377"></a>
<FONT color="green">378</FONT>        }<a name="line.378"></a>
<FONT color="green">379</FONT>    <a name="line.379"></a>
<FONT color="green">380</FONT>        /**<a name="line.380"></a>
<FONT color="green">381</FONT>         * Set &lt;code&gt;ranks[i] = Double.NaN&lt;/code&gt; for each i in &lt;code&gt;nanPositions.&lt;/code&gt;<a name="line.381"></a>
<FONT color="green">382</FONT>         *<a name="line.382"></a>
<FONT color="green">383</FONT>         * @param ranks array to modify<a name="line.383"></a>
<FONT color="green">384</FONT>         * @param nanPositions list of index values to set to &lt;code&gt;Double.NaN&lt;/code&gt;<a name="line.384"></a>
<FONT color="green">385</FONT>         */<a name="line.385"></a>
<FONT color="green">386</FONT>        private void restoreNaNs(double[] ranks, List&lt;Integer&gt; nanPositions) {<a name="line.386"></a>
<FONT color="green">387</FONT>            if (nanPositions.size() == 0) {<a name="line.387"></a>
<FONT color="green">388</FONT>                return;<a name="line.388"></a>
<FONT color="green">389</FONT>            }<a name="line.389"></a>
<FONT color="green">390</FONT>            Iterator&lt;Integer&gt; iterator = nanPositions.iterator();<a name="line.390"></a>
<FONT color="green">391</FONT>            while (iterator.hasNext()) {<a name="line.391"></a>
<FONT color="green">392</FONT>                ranks[iterator.next().intValue()] = Double.NaN;<a name="line.392"></a>
<FONT color="green">393</FONT>            }<a name="line.393"></a>
<FONT color="green">394</FONT>    <a name="line.394"></a>
<FONT color="green">395</FONT>        }<a name="line.395"></a>
<FONT color="green">396</FONT>    <a name="line.396"></a>
<FONT color="green">397</FONT>        /**<a name="line.397"></a>
<FONT color="green">398</FONT>         * Returns a list of indexes where &lt;code&gt;ranks&lt;/code&gt; is &lt;code&gt;NaN.&lt;/code&gt;<a name="line.398"></a>
<FONT color="green">399</FONT>         *<a name="line.399"></a>
<FONT color="green">400</FONT>         * @param ranks array to search for &lt;code&gt;NaNs&lt;/code&gt;<a name="line.400"></a>
<FONT color="green">401</FONT>         * @return list of indexes i such that &lt;code&gt;ranks[i] = NaN&lt;/code&gt;<a name="line.401"></a>
<FONT color="green">402</FONT>         */<a name="line.402"></a>
<FONT color="green">403</FONT>        private List&lt;Integer&gt; getNanPositions(IntDoublePair[] ranks) {<a name="line.403"></a>
<FONT color="green">404</FONT>            ArrayList&lt;Integer&gt; out = new ArrayList&lt;Integer&gt;();<a name="line.404"></a>
<FONT color="green">405</FONT>            for (int i = 0; i &lt; ranks.length; i++) {<a name="line.405"></a>
<FONT color="green">406</FONT>                if (Double.isNaN(ranks[i].getValue())) {<a name="line.406"></a>
<FONT color="green">407</FONT>                    out.add(Integer.valueOf(i));<a name="line.407"></a>
<FONT color="green">408</FONT>                }<a name="line.408"></a>
<FONT color="green">409</FONT>            }<a name="line.409"></a>
<FONT color="green">410</FONT>            return out;<a name="line.410"></a>
<FONT color="green">411</FONT>        }<a name="line.411"></a>
<FONT color="green">412</FONT>    <a name="line.412"></a>
<FONT color="green">413</FONT>        /**<a name="line.413"></a>
<FONT color="green">414</FONT>         * Represents the position of a double value in an ordering.<a name="line.414"></a>
<FONT color="green">415</FONT>         * Comparable interface is implemented so Arrays.sort can be used<a name="line.415"></a>
<FONT color="green">416</FONT>         * to sort an array of IntDoublePairs by value.  Note that the<a name="line.416"></a>
<FONT color="green">417</FONT>         * implicitly defined natural ordering is NOT consistent with equals.<a name="line.417"></a>
<FONT color="green">418</FONT>         */<a name="line.418"></a>
<FONT color="green">419</FONT>        private static class IntDoublePair implements Comparable&lt;IntDoublePair&gt;  {<a name="line.419"></a>
<FONT color="green">420</FONT>    <a name="line.420"></a>
<FONT color="green">421</FONT>            /** Value of the pair */<a name="line.421"></a>
<FONT color="green">422</FONT>            private final double value;<a name="line.422"></a>
<FONT color="green">423</FONT>    <a name="line.423"></a>
<FONT color="green">424</FONT>            /** Original position of the pair */<a name="line.424"></a>
<FONT color="green">425</FONT>            private final int position;<a name="line.425"></a>
<FONT color="green">426</FONT>    <a name="line.426"></a>
<FONT color="green">427</FONT>            /**<a name="line.427"></a>
<FONT color="green">428</FONT>             * Construct an IntDoublePair with the given value and position.<a name="line.428"></a>
<FONT color="green">429</FONT>             * @param value the value of the pair<a name="line.429"></a>
<FONT color="green">430</FONT>             * @param position the original position<a name="line.430"></a>
<FONT color="green">431</FONT>             */<a name="line.431"></a>
<FONT color="green">432</FONT>            public IntDoublePair(double value, int position) {<a name="line.432"></a>
<FONT color="green">433</FONT>                this.value = value;<a name="line.433"></a>
<FONT color="green">434</FONT>                this.position = position;<a name="line.434"></a>
<FONT color="green">435</FONT>            }<a name="line.435"></a>
<FONT color="green">436</FONT>    <a name="line.436"></a>
<FONT color="green">437</FONT>            /**<a name="line.437"></a>
<FONT color="green">438</FONT>             * Compare this IntDoublePair to another pair.<a name="line.438"></a>
<FONT color="green">439</FONT>             * Only the &lt;strong&gt;values&lt;/strong&gt; are compared.<a name="line.439"></a>
<FONT color="green">440</FONT>             *<a name="line.440"></a>
<FONT color="green">441</FONT>             * @param other the other pair to compare this to<a name="line.441"></a>
<FONT color="green">442</FONT>             * @return result of &lt;code&gt;Double.compare(value, other.value)&lt;/code&gt;<a name="line.442"></a>
<FONT color="green">443</FONT>             */<a name="line.443"></a>
<FONT color="green">444</FONT>            public int compareTo(IntDoublePair other) {<a name="line.444"></a>
<FONT color="green">445</FONT>                return Double.compare(value, other.value);<a name="line.445"></a>
<FONT color="green">446</FONT>            }<a name="line.446"></a>
<FONT color="green">447</FONT>    <a name="line.447"></a>
<FONT color="green">448</FONT>            /**<a name="line.448"></a>
<FONT color="green">449</FONT>             * Returns the value of the pair.<a name="line.449"></a>
<FONT color="green">450</FONT>             * @return value<a name="line.450"></a>
<FONT color="green">451</FONT>             */<a name="line.451"></a>
<FONT color="green">452</FONT>            public double getValue() {<a name="line.452"></a>
<FONT color="green">453</FONT>                return value;<a name="line.453"></a>
<FONT color="green">454</FONT>            }<a name="line.454"></a>
<FONT color="green">455</FONT>    <a name="line.455"></a>
<FONT color="green">456</FONT>            /**<a name="line.456"></a>
<FONT color="green">457</FONT>             * Returns the original position of the pair.<a name="line.457"></a>
<FONT color="green">458</FONT>             * @return position<a name="line.458"></a>
<FONT color="green">459</FONT>             */<a name="line.459"></a>
<FONT color="green">460</FONT>            public int getPosition() {<a name="line.460"></a>
<FONT color="green">461</FONT>                return position;<a name="line.461"></a>
<FONT color="green">462</FONT>            }<a name="line.462"></a>
<FONT color="green">463</FONT>        }<a name="line.463"></a>
<FONT color="green">464</FONT>    }<a name="line.464"></a>




























































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